ArticleMethods and protocols2020
Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis.
Article in Methods and protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
4 citing papers in PubMed.
- met v1: expanding on old estimations of biodiversity from eDNA with a new database framework.Database : the journal of biological databases and curation · 2022Article
- Using metatranscriptomics to estimate the diversity and composition of zooplankton communities.Molecular ecology resources · 2022Article
- Life barcoded by DNA barcodes.Conservation genetics resources · 2022Review
- Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction.Frontiers in molecular biosciences · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of next-generation sequencing has allowed for higher-throughput determination of which species live within a specific location. Here we establish that three analysis methods for estimating diversity within samples-namely, Operational Taxonomic Units; the newer Amplicon Sequence Variants; and a method commonly found in sequence analysis, minhash-are affected by various properties of these sequence data. Using simulations we show that the presence of Single Nucleotide Polymorphisms and the depth of coverage from each species affect the correlations between these approaches. Through this analysis, we provide insights which would affect the decisions on the application of each method. Specifically, the presence of sequence read errors and variability in sequence read coverage deferentially affects these processing methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.